đŸ”Ŧ Chimeric Detective Report

Comprehensive Analysis of Chimeric Contigs in Viral Metagenomic Assembly

6
Contigs Analyzed
5
Contigs Split
0
Contigs Preserved
0.8
Mean Confidence

📊 Summary Visualizations

Chimera Type Distribution

Confidence Score Distributions

Decision Summary

Evidence Types Overview

🔍 Detailed Analysis Results

Contig ID Chimera Type Confidence Decision Breakpoint Evidence Types Explanation
chimeric_001 technical_artifact 0.8 SPLIT 1000 kmer_composition_change, gc_content_shift
Contig chimeric_001 shows clear evidence of being a technical chimera resulting from misassembly. At position 1,000, there is a 1.2x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.38) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.77.
chimeric_002 technical_artifact 0.8 SPLIT 1000 kmer_composition_change, gc_content_shift
Contig chimeric_002 shows clear evidence of being a technical chimera resulting from misassembly. At position 1,000, there is a 1.2x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.33) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.77.
chimeric_002 technical_artifact 1.0 SPLIT 1500 kmer_composition_change, gc_content_shift
Contig chimeric_002 shows clear evidence of being a technical chimera resulting from misassembly. At position 1,500, there is a 1.2x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.28) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.64.
chimeric_003 technical_artifact 0.7 SPLIT 1500 kmer_composition_change, gc_content_shift
Contig chimeric_003 shows clear evidence of being a technical chimera resulting from misassembly. At position 1,500, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.37) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.68.
chimeric_004 technical_artifact 0.7 SPLIT 1500 kmer_composition_change, gc_content_shift
Contig chimeric_004 shows clear evidence of being a technical chimera resulting from misassembly. At position 1,500, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.28) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.68.
chimeric_005 technical_artifact 0.8 SPLIT 1000 kmer_composition_change, gc_content_shift
Contig chimeric_005 shows clear evidence of being a technical chimera resulting from misassembly. At position 1,000, there is a 1.2x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.23) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.79.

📈 Individual Contig Details

Click on the links below to view detailed analysis for each chimeric contig:

ℹī¸ Methodology & Interpretation

Detection Methods

Chimeric contigs are detected using multiple complementary approaches:

  • Coverage Discontinuities: Sharp changes in read coverage depth
  • Sequence Composition: Changes in GC content and k-mer frequencies
  • Taxonomic Classification: Transitions between different viral/host lineages
  • Read Pair Orientation: Inconsistent paired-end read orientations

Classification Categories

  • Technical Artifacts: Assembly errors, typically split
  • PCR Chimeras: Amplification artifacts, typically split
  • Biological Recombination: Genuine recombination events, preserved
  • Provirus Integration: Virus-host integration sites, flagged

Confidence Scores

Confidence scores range from 0-1, with higher scores indicating stronger evidence for the classification. Scores above 0.8 are considered high confidence, 0.5-0.8 medium confidence, and below 0.5 low confidence.